Articles pubs.acs.org/acschemicalbiology
Quantitative Chemical Proteomic Profiling of the in Vivo Targets of Reactive Drug Metabolites Landon R. Whitby,*,† R. Scott Obach,‡ Gabriel M. Simon,§ Matthew M. Hayward,*,‡ and Benjamin F. Cravatt*,† †
The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, California 92307, United States ‡ Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States § Vividion Therapeutics, 3033 Science Park Rd Suite D, San Diego, California 92121, United States S Supporting Information *
ABSTRACT: Idiosyncratic liver toxicity represents an important problem in drug research and pharmacotherapy. Reactive drug metabolites that modify proteins are thought to be a principal factor in drug-induced liver injury. Here, we describe a quantitative chemical proteomic method to identify the targets of reactive drug metabolites in vivo. Treating mice with clickable analogues of four representative hepatotoxic drugs, we demonstrate extensive covalent binding that is confined primarily to the liver. Each drug exhibited a distinct target profile that, in certain cases, showed strong enrichment for specific metabolic pathways (e.g., lipid/ sterol pathways for troglitazone). Site-specific proteomics revealed that acetaminophen reacts with high stoichiometry with several conserved, functional (seleno)cysteine residues throughout the liver proteome. Our findings thus provide an advanced experimental framework to characterize the proteomic reactivity of drug metabolites in vivo, revealing target profiles that may help to explain mechanisms and identify risk factors for drug-induced liver injury.
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and thus constitutes an impediment to drug development. Despite these serious issues, our understanding of the mechanisms of DILI remains limited,6 and there is consequently a need for new methodologies to identify and characterize drugs at risk for reactive metabolism in vivo. Strong correlative evidence supports that reactive metabolites play an underlying causative role in many cases of DILI.7,8 The reactive metabolites are thought to promote toxicity through the covalent modification and functional perturbation of liver proteins. Covalent protein adduction by reactive metabolites may also promote diverse immunogenic responses by generating drug-derived antigens.7,9 Concerns over the functional perturbation of liver proteins and aberrant promotion of autoimmune responses has motivated the drug discovery industry to adopt a strategy where chemical functionalities
dverse drug reactions are a common and often dangerous complication that can lead to unpredictable life-threatening injury and drug withdrawal at advanced stages of development.1,2 Some toxicological effects reflect parent drug action at primary targets or off-targets, leading to predictable and monitorable outcomes. A distinct type of high-risk adverse drug effect occurs primarily in the liver, where enzymatic metabolism can convert drugs to chemically reactive metabolites that covalently modify proteins. The chemical stress produced by reactive drug metabolites is considered to be a primary cause of drug-induced liver injury (DILI).3 DILI is the most common adverse drug reaction and the cause of over half of all cases of acute liver failure in the United States.4 Hepatotoxicity can manifest as a reproducible and dosedependent phenomenon (as with acetaminophen) or can arise idiosyncratically in small numbers of individuals after a drug is used in large populations.5 The appearance of idiosyncratic DILI during late clinical testing or postmarketing can lead to the unexpected withdrawal of drugs after significant investment © XXXX American Chemical Society
Received: April 27, 2017 Accepted: June 5, 2017
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DOI: 10.1021/acschembio.7b00346 ACS Chem. Biol. XXXX, XXX, XXX−XXX
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Figure 1. Structures and initial profiling of the reactivity of chemical proteomic probes for hepatoxic drugs. (A) Structures of the parent hepatotoxic drugs (1−4) and their corresponding alkyne-modified (clickable) probes (5−8). The alkyne functionality was incorporated at sites intended to minimize interference with the known routes of metabolism of the drugs; see Figure S1 for more details. (B) In vitro reactivity profiles for probes 5− 8 in mouse liver lysates with or without NADPH. Freshly prepared mouse liver proteome (2 mg mL−1) was treated with DMSO or indicated probes (0.1−50 μM, 2 h, RT), and protein reactivity events analyzed by CuAAC with an azide-rhodamine tag followed by SDS-PAGE and in-gel fluorescence scanning (fluorescent gels shown in grayscale). See Figure S2A for a lower intensity image of the gel. (C) Schematic for chemical proteomic workflow used to profile the in vivo reactivity of probes 5−8. Following treatment with vehicle or probes (i.p., 2 h), mice were sacrificed and liver proteomes prepared and analyzed for protein reactivity events as described in part B. (D) Concentration-dependent reactivity of mouse liver soluble (left) and membrane (right) proteomes following treatment of mice with vehicle or probes 5−8 (i.p., 2 h) at the indicated doses. The dosing range for probe 8 was extended into the acute hepatoxic range for acetaminophen (300 mg/kg). (E) Proteomic reactivity of five tissues from mice treated with vehicle or probes 5−8 (i.p., 90 mg/kg, 2 h). Data shown are for soluble proteomes; see Figure S2B for membrane proteome reactivity data. (F) Proteomic reactivity of liver from mice treated for the indicated number of days with vehicle or probes 5−7 (30 mg/kg, i.p., once daily). Data shown are for membrane proteomes; see Figure S2C for soluble proteome reactivity data.
assigning the identified proteins as targets of reactive metabolites. These deficiencies could be addressed by incorporating latent affinity handles into drugs of interest to facilitate the enrichment of reactive metabolite-modified proteins over background proteins. We, and others, have adopted this type of chemical proteomic strategy to globally map the protein targets of electrophilic drugs,15 environmental chemicals,16 and natural products.17 In these studies, drugs are modified with simple alkyne or azide groups so that reactive proteins can then be conjugated to reporter tags (fluorophore or biotin) using the copper-catalyzed azide−alkyne cycloaddition (CuAAC) reaction18 for subsequent proteomic profiling by gel- or mass spectrometry (MS)-based methods.19 Incorporating isotopic labels into the MS-based proteomic workflow further enables quantification of electrophilic drug− protein reactions with good precision and often site (residue)specific resolution.20 Here, we have applied quantitative chemical proteomics to globally map the protein targets of several hepatotoxic drugs in mice. Alkyne analogues of each drug were synthesized and found to react with distinct sets of liver proteins in vivo, indicating that reactive drug metabolites retain a substantial recognition component that influences their protein interactions. Some drugs showed a strong preference for targeting specific biochemical pathways, and in the case of acetaminophen, we provide evidence for high-occupancy modification of
with the potential to undergo reactive metabolism are designated as “structural alerts” and avoided in lead optimization, as well as the implementation of in vitro screens for reactive metabolites and covalent drug−protein adducts.10 Strict avoidance of drugs with reactive metabolites, however, can place an undue burden on drug research programs and halt the development of useful new medicines. A more nuanced approach that considers parameters such as drug dose, alternative routes of metabolism and clearance, and the risk− benefit related to specific therapeutic indications can guide decisions on advancing drugs with reactive metabolites.6 Such judgments would also benefit from a more complete understanding of the proteins targeted by reactive metabolites in vivo and how the adduction of these proteins mechanistically relates to the end point of liver toxicity. The identification of protein targets of reactive metabolites commonly involves the use of radiolabeled drugs, which are administered to animal or cell models and drug-adducted proteins then detected by one- or two-dimensional SDS-PAGE and autoradiography. Proteins comigrating with radioactive signals are then excised from the gel and identified by mass spectrometry (MS) methods.11,12 While this general approach has been employed to identify proteins modified by several drugs that produce DILI,13,14 it suffers from limitations that include poor sensitivity and resolution, resulting in a bias toward detecting high-abundance proteins and ambiguity in B
DOI: 10.1021/acschembio.7b00346 ACS Chem. Biol. XXXX, XXX, XXX−XXX
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Figure 2. Quantitative MS-based characterization of the in vivo proteome reactivity of hepatotoxic drugs. (A) Schematic of the workflow for quantitative MS-based proteomic experiments to identify mouse liver proteins modified by probes 5−8 in vivo. Mice were treated with the probes 5− 8 or the corresponding parent drugs 1−4 using acute (8 or 4, 200 mg/kg, 2 h) or subchronic (5−7 or 1−3, 30 mg/kg, 7 days, q.d) dosing conditions. Following sacrifice of the animals, liver proteomes were prepared and probe-modified proteins conjugated by CuAAC to an azide-biotin tag, enriched using streptavidin, and digested on-bead with trypsin and the resulting tryptic peptides isotopically labeled at the N-terminus and lysine ε-amino groups by reductive dimethylation (ReDiMe) with “heavy” (D2C13O, probe-treated sample) or “light” (H2CO, control sample) formaldehyde. LC-MS/MS analysis of the combined heavy and light samples enabled identification and quantification of proteins based on MS2 and MS1 signals, respectively. (B) Representative ReDiMe ratio plot for proteins identified from mice treated with probe 8 (heavy) versus drug 4 (light, control). Proteins with heavy/light ratios (or R values) ≥ 4 (dashed red line) were considered covalent targets of probe 8. See Figure S3 for the corresponding ReDiMe ratio plots for probes 5−7. (C) Bar graph depicting the number of protein targets for the indicated probes in mouse liver. (D) Left bar, stacked bar graph showing the aggregate number of protein targets of probes 5−8 and the fraction of these targets enriched by one or more probes. Right bar, fraction of protein targets of probes 5−8 representing proteins previously identified as targets of chemically reactive metabolites in mice, as assessed by the presence in the Target Protein Database (TPDB; http://targetprotein.res.ku.edu). (E) Stacked bar graph depicting the shared and unique protein targets of probes 5−8 in mouse liver. (F) Bar graph comparing the percentage of proteins containing an annotated functional cysteine residue in the Uniprot Knowledgebase for all mouse proteins (3%) versus proteins identified as targets of probes 5−8 (15%). (G) Stacked bar depicting the percentage of protein targets of probes 5−8 for which orthologous human proteins were identified (combined red and blue sections) and found to be targets of cysteine-directed fragment electrophiles (blue section) in a recent chemical proteomic study.28 (H) Bar graph depicting the percentage of protein targets of probes 5, 6, and 8 that are involved in the indicated primary metabolic processes, according to the PANTHER classification system (http://pantherdb.org). The protein targets were first classified by biological process (Figure S4A), which revealed a major subset of targets (∼60% for all combined probes) classified as metabolic. These metabolic targets were further categorized by a metabolic process, and the majority (∼70% for all combined probes) were listed as primary metabolic (Figure S4B). The data in panel H represent further classification of these metabolic targets into subcategories of primary metabolic processes.
Figure S1A). Metabolite identification and metabolic stability experiments in the S9 fraction of mouse liver tissue confirmed that the parent drugs 1−4 and their respective alkynylated probes 5−8 form analogous metabolites, including glutathione (GSH) adducts of these metabolites,25 and display similar overall metabolic stability (Figure S1B and Table S1). We initially evaluated the in vitro proteomic reactivity of 5−8 by exposing the probes (0.1−50 μM) to mouse liver homogenates in the presence or absence of NADPH (a cofactor for CYP enzymes) for 2 h, followed by CuAAC coupling to an azide-rhodamine reporter tag, SDS-PAGE, and in-gel fluorescence scanning. Each probe displayed a distinct concentration-dependent proteomic reactivity profile that was much stronger in the presence of NADPH (Figures 1B and S2A), consistent with metabolic activation being mediated, as expected, by CYP enzymes. We next examined the in vivo proteomic reactivity of 5−8 by treating mice with the probes (10−90 mg/kg, i.p., with probe 8 also being evaluated at 200 and 300 mg/kg) for 2 h, followed by isolation of liver tissue and
functional (seleno)cysteine residues in diverse liver proteins. Our findings, taken together, thus highlight the value of indepth mapping of protein targets of reactive drug metabolites in vivo to identify new risk factors and possible mechanistic underpinnings for DILI.
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RESULTS Clickable Probes for in Vivo Profiling of Reactive Metabolites. As case studies for examining the in vivo proteomic reactivity of hepatotoxic compounds, we selected three drugs known to cause idiosyncratic DILItroglitazone (1), clozapine (2), and tienilic acid (3)as well as the acute hepatotoxin acetaminophen (4) (Figure 1A). Each of these drugs undergoes metabolic activation, mostly mediated by cytochrome P450 (CYP) enzymes, to produce reactive metabolites that covalently bind to proteins.21−24 We designed and synthesized alkynylated analogues of each drug where the installed alkynes were positioned to avoid interference with established pathways for metabolic activation (Figure 1A and C
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quantified in data sets from at least three of the four tested probes or was strongly and consistently enriched by a single probe (≥10 total quantified peptides with detection in both replicate experiments), to be part of the target overlap analysis. Of the 152 aggregate targets of probes 5−8, 126 met this requirement, and notably, 70% (91) of these proteins were enriched by only a single probe, with the remaining ∼30% of proteins being mostly enriched by two probes (30 proteins) along with a few (five proteins) enriched by three probes (Figure 2D). Only a handful of the 152 targets of probes 5−8 are found in a reactive metabolite target protein database (TPDB; http://targetprotein.res.ku.edu/;27 Figure 2D), which has mostly been assembled from studies performed with radiolabeled drugs. A deeper analysis of target overlap revealed that probes 6 and 8 shared many targets, while the target profile of probe 5 consisted mostly of unique targets (Figure 2E), including serum albumin (Figure S3), matching the ∼70 kDa probe-5-labeled protein detected in most tissues (Figure 1E). Even though probe 7 only enriched nine targets, some of these proteins were unique to this probe (Figure 2E). Functional Classification of Protein Targets of Reactive Metabolites. A unifying theme for the targets across all reactive metabolite probes was an enrichment for proteins containing functional (seleno)cysteine residues, including those annotated in the UniprotKB as active-site, redox-active disulfide, or post-translationally modified (Figure 2F). A substantial number of the probe targets also showed evidence of covalent ligandability in a recent proteome-wide assessment of cysteine-directed fragment electrophiles using competitive profiling with a broad-spectrum iodoacetamide (IA)-alkyne probe28 (Figure 2G). These findings are consistent with previous work demonstrating that (i) reactive metabolites of drugs, including several of the drugs tested herein, have a propensity to covalently modify cysteine residues23,24,29 and (ii) functional cysteines have, in general, higher intrinsic reactivity and consequently greater potential for covalent ligand modification compared to other cysteines in the proteome.28,30 We also note that the targets of reactive metabolite probes included several proteins with conserved, functional selenocysteine residues; for instance, six selenoproteins (TXNRD1, VIMP, SEPHS2, SELT, TXNRD3, and SELO) were enriched by probe 8, including thioredoxin reductase 1 (TXNRD1), which was recently described as a covalent target of reactive metabolites of acetaminophen.31 We next asked whether the targets of reactive metabolite probes showed enrichment for specific biological processes using the PANTHER classification system,32 which revealed that the vast majority of probe targets were involved in primary metabolic processes (Figure S4A, B). This output may reflect enrichment for cysteine-dependent proteins within metabolic processes or simply attributed to the high metabolic composition of the liver proteome. Further inspection revealed that individual probes enriched proteins from different primary metabolic pathways. Probe 5, for instance, showed a striking preference for proteins involved in lipid or steroid metabolism, while probes 6 and 8 exhibited greater enrichment of proteins involved in amino acid and protein metabolism (Figure 2H). These results suggest that the features of troglitazone that promote interactions with its primary targetsthe lipidactivated nuclear receptors PPARsmay also endow the metabolic products of this drug with preferential binding to and reactivity with other lipid-interacting proteins.
gel-based analysis of probe-modified proteins (Figure 1C). Each probe produced substantial, dose-dependent protein reactivity in mouse liver, and, as was observed in vitro, the profiles of modified proteins differed for each probe in vivo (Figure 1D). The overall extent of proteomic reactivity also differed markedly for probes in vitro versus in vivo. The troglitazone (5) and tienilic acid (7) probes, for instance, showed strong protein reactivity in liver homogenates (Figure 1B) but more tempered protein labeling profiles in vivo (Figure 1D). In contrast, the acetaminophen probe (8) exhibited extensive protein labeling in vivo (Figure 1D) but limited in vitro reactivity in liver homogenates (Figure 1B). Probes 5−8 showed very limited in vivo proteomic reactivity in other mouse tissues (Figures 1E and S2B), consistent with the predominant expression of CYPs in liver and the corresponding CYPgenerated metabolites being restricted in reactivity to proteins in this tissue. One exception was a probe 5-labeled 70 kDa protein that appeared in every tissue, which we later confirmed by MS analysis to be serum albumin (see below), an abundant protein that is produced in liver and then secreted into the blood, likely accounting for its detection in other tissues. We also determined if probes 5−7 showed cumulative protein reactivity in the liver following multiday dosing in mice. Mice were treated with probes or vehicle once per day (30 mg/ kg, i.p.) for 1, 3, or 7 days and then sacrificed, and liver proteomes were analyzed for protein reactivity by gel-based analysis. Each probe showed evidence of cumulative protein labeling over the seven-day treatment period, with particularly striking increases in liver protein reactivity being observed for probes 5 and 6 (Figures 1F and S2C). Having found by gel-based profiling that clickable analogues of hepatoxic drugs provide probes for visualizing reactive metabolite-protein interactions in liver both in vitro and in vivo, we next focused on identifying the probe-modified proteins using quantitative MS methods. Identification of Protein Targets of Reactive Metabolites. To identify proteins modified by probes 5−8 in vivo, we treated pairs of mice with a probe or the corresponding parent drug under acute (8 or 4, 200 mg/kg, 2 h) or subchronic (5−7 or 1−3, 30 mg/kg, 7 days, q.d.) dosing conditions. Comparator mice were treated with the parent drug (rather than vehicle) to control for potential drug-induced gene and protein expression in liver tissue. Probe-modified proteins were then identified from liver tissue of mice by CuAAC coupling to an azide-biotin tag, streptavidin enrichment, and quantitative LC-MS using amine reductive-dimethylation (ReDiMe) chemistry26 to incorporate isotopically “heavy” or “light” methyl groups into the tryptic peptides of proteins from probe- versus controltreated mice, respectively (Figure 2A). Targets of each probe were defined as proteins showing 4-fold or higher ReDiMe ratios (or R values) in probe- vs parent-drug-treated mice (Figures 2B and S3A−C and Tables S2 and S3; n = 2/group). Under the tested conditions, and generally consistent with the gel-based profiles of protein labeling events in mouse liver (Figure 1D,F), probes 5, 6, and 8 exhibited similarly high proteomic reactivity (∼50−80 targets each), while probe 7 displayed fewer protein modification events (nine targets; Figure 2C and Table S2). We next examined the overlap across the target profiles of the tested hepatotoxic drugs. Here, we took caution to minimize the potential for stochastic protein detection by LC-MS to alter our estimates of unique vs overlapping targets for probes 5−8. Accordingly, we required that a protein was D
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Figure 3. Characterization of the proteomic reactivity of the troglitazone probe 5 in human hepatocytes. (A) Analysis of the membrane and soluble proteomic reactivity of primary human hepatocytes treated with vehicle (DMSO) or probe 5 (20 μM, 4 h). (B) A ReDiMe ratio plot for proteins enriched and identified from human hepatocytes treated with probe 5 (heavy) versus compound 1 (control, light) with corresponding probe/control (heavy/light isotopic) ratios. Proteins with R values ≥ 4 (dashed red line) were considered covalent targets of probe 5. (C) Venn diagram demonstrating the overlap of orthologous or homologous proteins found to be targets of probe 5 in both mouse liver and human hepatocytes. (D) Bar graph depicting the percentage of protein targets of probe 5 from human hepatocytes that are involved in the indicated primary metabolic processes, according to the PANTHER classification system. The protein targets were first classified by a biological process, which revealed a major subset (∼65%) classified as metabolic (Figure S4C). Further categorization indicated that 75% of the metabolic targets were involved in primary metabolic processes (Figure S4D). The data in panel D represents further classification of these metabolic targets into subcategories of primary metabolic processes.
We finally asked if the chemical proteomic analysis of reactive metabolite targets could be extended to freshly isolated human hepatocytes using probe 5 as a case study. Primary human hepatocytes were treated in situ with probe 5 (20 μM, 4 h) or compound 1, followed by CuAAC coupling to an azide-
Rh tag, SDS-PAGE, and in-gel fluorescence scanning, which revealed extensive proteomic reactivity for probe 5 (Figure 3A). We followed up this gel-based study with a quantitative LC-MS (ReDiMe) analysis, which identified >200 protein targets of probe 5 (R value ≥ 4) in human hepatocytes (Figure 3B). The E
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Figure 4. Characterization of high-occupancy protein reactivity events for acetaminophen (4) in mouse liver. (A) Gel-based profile of competitive blockade of probe 8 reactivity with mouse liver proteins by acetaminophen (4). Mice were treated with vehicle or 4 at the indicated dose (2 h, i.p.), followed by treatment with probe 8 (100 mg/kg, 1 h, i.p.). Animals were then sacrificed and liver soluble and membrane protein fractions conjugated to rhodamine-azide by CuAAC and analyzed by SDS-PAGE and in-gel fluorescence scanning. Arrows mark proteins for which probe 8 reactivity was competed by pretreatment with 4. (B) A ReDiMe ratio plot for proteins identified from liver tissue of mice treated with 4 (500 mg/kg, 2 h, i.p.; light) or vehicle (heavy), followed by probe 8 (100 mg/kg, 1 h, i.p.). Proteins with R values ≥ 3 (dashed red line) were considered to be competitively blocked in reactivity with probe 8 and designated as high-occupancy targets of 4 (shown in the magnified region on the right). Highoccupancy targets containing catalytic cysteine or selenocysteine residues are shown in red and blue, respectively.
Figure 5. Comparative proteomic reactivity profiling of acetaminophen and its less toxic analogue AMAP. (A) Structures of AMAP (9) and the alkyne-modified probe analogue 10. (B) Comparative gel-based analysis of the mouse liver proteomic reactivity of probes 8 and 10 in vivo. Mice were treated with the indicated probe and dose (10−300 mg/kg, 2 h, i.p.) and sacrificed and liver soluble and membrane protein fractions conjugated to rhodamine-azide by CuAAC and analyzed by SDS-PAGE and in-gel fluorescence scanning. (C) A ReDiMe ratio plot for proteins identified from liver tissue of mice treated with 4 or 9 (400 mg/kg, 2 h, i.p.), followed by 8 (100 mg/kg, 1 h, i.p.). Dashed red lines designated proteins with log2 R values > 1 (preferentially competed by 4) or < 1 (preferentially competed by 9). Six of the 14 proteins preferentially competed by 4 were selenocysteine-containing proteins (shown in blue).
number of protein targets identified for probe 5 in suspended primary human hepatocytes was substantially larger than that found in the liver from mice treated with this probe (>200 vs ∼50), which could reflect that the concentration of probe used in the human hepatocyte treatments (20 μM) exceeded the probe exposure in vivo or that the metabolic activation of probe 5 was more efficient in human hepatocytes. Regardless, we observed good consistency in targets identified in both systems, as orthologues and homologues of many mouse protein targets were enriched by probe 5 in human hepatocytes (Figure 3C). Also, as was observed in mouse liver tissue, the targets of probe 5 in human hepatocytes showed substantial enrichment for
proteins involved in lipid and steroid metabolism (Figures 3D and S4C,D). Assessing the Stoichiometry of Reactive Metabolite− Protein Interactions in Vivo. While covalent protein binding may contribute to drug toxicity by creating immunogenic adducts, it is also possible that reactive metabolites perturb the specific functions of individual proteins, especially if metabolite reactions occur at high stoichiometry with these proteins. We therefore sought to complement our chemical proteomic analysis of proteins modified by reactive metabolites with determination of the fractional engagement of these modification events in vivo. As a case study, we evaluated the hepatotoxin acetaminophen (4). F
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Table 1. High-Occupancy Protein Targets of Acetaminophen 4 in Mouse Liver As Determined by Quantitative MS-Based Proteomicsa entry
Uniprot ID
gene name
probe 8 enriched, whole protein
4 competed, whole protein analysis
4 competed, peptide analysis
competed residue(s), peptide
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
Q9CXT8 Q9D172 P17751 Q9DBC0 O09131 Q9JMH6 P62342 O09172 Q9CRB3 Q8BRK8 Q791 V5 Q8VHE0 Q8BUV3 Q8VCF0 Q99LX0 Q9DBA6 E9Q3C1 Q9WV55 O08573 P42227 Q922Q1 O70252 Q9JLJ1 Q8VC19 O08997 P97821 Q9JLC3 G5E860 Q8BH00 Q9JLT4 Q9JLJ2 P47738 Q9BCZ4 Q9ESW8 Q8CDN6 E9Q137
Pmpcb D10Jhu81e Tpi1 Selod Gsto1d Txnrd1d Seltd Gclm Urah Prkaa2 Mtch2 Sec63 Gphn Mavs Park7d Tysnd1 C2cd2 Vapa Lgals9 Stat3d Marc2 Hmox2d Selkd Alas1d Atox1d Ctscd Msrb1d Usp16d Aldh8a1d Txnrd2d Aldh9a1d Aldh2d Vimpd Pgpep1d Txnl1d Tex264d
20 20 20 10 20 20 20 12 20 5.7 6.6 8.8 9.2 20 11 5.6 20 4.3 4.8 5.8 4.4 20 ND ND ND ND ND ND 1.9 1.8 1.7 1.5 20 20 20 7.1
20 20 11 20 8.0 20 20 4.9 3.7 3.1 NC NC NC NC NC NC NC NC NC NC NC ND ND ND ND ND ND ND 1.5 1.6 1 0.9 20 20 4.7 3.5
20 20 13,b 20c 18,b 20c 1.2,b 20c 5.5,b 6.5c 4.3 3.8 2.8,b 6.4c 4.0 3.4, 5.5 7.5b, 20c 3.9,b 14c 4.8 4.4 3.6 3.6 3.5 3.4 3.2 2.4,b 4.0c 4.4 7.9 5.6 4.8 3.4 3.4 3.3 11,b 12c 3.5,b 4c 3.9 3.8,b 3.5c ND ND ND ND
C248b C174c C71b,c U665b,c C32b,c U612b,c U49b C35b C35b,c C413b C296b, C56b C295b,c C452b,c C470b C106b C106/C110b C408b C60b C138b C259b C74b,c C281b U497b C108b C12/C15b C254/C257b U95b C204b C287/289b,c U497b,c C288/289b C320−322b,c
a NC, not competed; ND, not detected. bMeasured by competition with IA alkyne probe (in vitro treatment). cMeasured by competition with probe 8 (in vivo treatment). dContains conserved functional (seleno)cysteine residue.
overall covalent protein binding in rodent liver as assessed by radiolabeled protein binding assays.33 We first compared the protein reactivity profiles of liver proteomes from mice treated with 8 or 1025 (an alkyne probe analogue of 9; Figure 5A; 10− 300 mg/kg, 2 h), which revealed that the magnitude of covalent reactivity of probe 8 greatly exceeded that of probe 10 (Figure 5B). Because previous studies have indicated that the protein adducts formed by 9 may be less stable under conditions of gel electrophoresis compared to the protein adducts of 4,33 we next assessed the fractional engagement of 8-labeled liver proteins by 9 in vivo (400 mg/kg, 2 h) using quantitative (ReDiMe) MSbased proteomics, which revealed that 9 shared several highoccupancy targets with 4 (Table S2). We then directly compared 4 versus 9 for their respective competitive blockade of protein labeling by 8 in vivo. In these experiments, mice were treated with 4 or 9 (400 mg/kg, 2 h) followed by 8 (100 mg/ kg, 1 h) and their liver tissues compared by quantitative (ReDiMe) MS-based proteomics. Plotting the R values (log 2) for 9-treated/4-treated mice (where 0 = no differences; >1 =
Our original enrichment experiments identified 82 targets of the acetaminophen probe 8 in mouse liver (Figure 2C). We next assessed the fractional engagement of these events by treating mice with a dose range of 4 (200−600 mg/kg, 2 h) followed by probe 8 (100 mg/kg, 1 h). Gel-based analysis of these “competition” profiling experiments revealed that 4 produced a concentration-dependent blockade of probe-8labeling for a subset of proteins in the liver proteome (Figure 4A). We identified these 4-competed proteins by quantitative MS-based proteomics of liver tissue from mice treated with 4 (500 mg/kg, 2 h) or vehicle followed by probe 8 (100 mg/kg, 1 h; Figure 4B, where high-occupancy targets of 4 were defined as proteins showing R values > 3 for vehicle/4 comparisons). The high-engagement protein targets of 4 included several selenoproteins and proteins that use conserved cysteine residues for catalysis (Figure 4B). The acetaminophen isomer N-acetyl-m-aminophenol (AMAP, 9; Figure 5A) does not show hepatotoxicity in mice, even though both 4 and 9 have been reported to exhibit similar G
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the processing of liver tissue prior to in vitro analysis by isoTOP-ABPP. These results provide further evidence that acetaminophen (4) generates high-engagement adducts with functional (seleno)cysteines in several liver proteins in vivo and also reveal complementary features of data obtained by whole protein enrichment (e.g., competition with probe 8) versus sitespecific (e.g., isoTOP-ABPP) chemical proteomic experiments.
preferentially competed by 4;
